Ecological persistence interrupted in Caribbean coral reefs

The recent mass mortality of Caribbean reef corals dramatically altered reef community structure and begs the question of the past stability and persistence of coral assemblages before human disturbance began. We report within habitat stability in coral community composition in the Pleistocene fossil record of Barbados for at least 95 000 years despite marked variability in global sea level and climate. Results were consistent for surveys of both common and rare taxa. Comparison of Pleistocene and modern community structure shows that Recent human impacts have changed coral community structure in ways not observed in the preceding 220 000 years.     

Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution

The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes.     

Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~ 1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.     

Glycine to glutamic acid misincorporation observed in a recombinant protein expressed by Escherichia coli cells

A novel amino acid misincorporation, in which the intended glycine (Gly) residues were replaced by a glutamic acid (Glu), was observed in a recombinant protein expressed by Escherichia coli. The misincorporation was identified by peptide mapping and liquid chromatography-tandem mass spectrometric analysis on proteolyzed peptides of the protein and verified using the corresponding synthetic peptides containing the misincorporated residues. Analysis of the distribution of the misincorporated residues and their codon usage shows strong correlation between this misincorporation and the use of rarely used codon within the E. coli expression system. Results in this study suggest that the usage of the rare codon GGA has resulted in a Glu for Gly misincorporation.     

Biosorption and desorption of lanthanum(III) and neodymium(III) in fixed-bed columns with Sargassum sp.: perspectives for separation of rare earth metals

Rare earth (RE) metals are essentials for the manufacturing of high-technology products. The separation of RE is complex and expensive; biosorption is an alternative to conventional processes. This work focuses on the biosorption of monocomponent and bicomponent solutions of lanthanum(III) and neodymium(III) in fixed-bed columns using Sargassum sp. biomass. The desorption of metals with HCl 0.10 mol L(-1) from loaded biomass is also carried out with the objective of increasing the efficiency of metal separation. Simple models have been successfully used to model breakthrough curves (i.e., Thomas, Bohart-Adams, and Yoon-Nelson equations) for the biosorption of monocomponent solutions. From biosorption and desorption experiments in both monocomponent and bicomponent solutions, a slight selectivity of the biomass for Nd(III) over La(III) is observed. The experiments did not find an effective separation of the RE studied, but their results indicate a possible partition between the metals, which is the fundamental condition for separation perspectives.     

Realistic losses of rare species disproportionately impact higher trophic levels

Predicting the consequences of changes in biodiversity requires understanding both species' susceptibility to extirpation and their functional roles in ecosystems. However, few studies have evaluated the effects of realistic, non-random biodiversity losses, severely limiting the applicability of biodiversity research to conservation. Here, we removed sessile species from a rocky shore community in a way that deliberately mimicked natural patterns of species loss. We found that the rarest species in the system act from the bottom up to disproportionately impact the diversity and abundance of consumers. Realistic losses of rare species in a diverse assemblage of seaweeds and sessile invertebrates, collectively comprising <10% of sessile biomass, resulted in a 42-47% decline in consumer biomass. In contrast, removal of an equivalent biomass of dominant sessile species had no effect on consumers. Our results highlight the 'cornerstone' role that rare species can play in shaping the structure of the community they support.     

Conservation of Britain's biodiversity: the case of Hieracium cyathis (Asteraceae) and its relation to other apomictic taxa

Hieracium cyathis (Ley) W. R. Linton (Asteraceae), Chalice Hawkweed, is a rare species endemic to Britain. It is a distinct member of Hieracium Section Oreadea , characterized by a short acladium and out-curved tips to the phyllaries. Historic records and current field survey indicate it has occurred in two localities in SW England and seven in South Wales. It is still present in all sites except for one Welsh locality, is significantly threatened at Cheddar Gorge, and two Welsh sites have only three plants each. Comparative morphology, cultivation experiments and amplified fragment length polymorphism (AFLP) analysis do not support the reported differences between material from SW England and Wales. AFLP analysis showed that every plant in the field was genetically similar but different, and minor genetic variation was found in one progeny array. It is a triploid (2 n  = 27) with apomictic seed production, and 26% potentially viable pollen. It qualifies as 'Near Threatened' under the 2001 IUCN threat criteria. General guidelines for conservation of microspecies of Hieracium are discussed.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 669–680.     

Phosphatized rare star-like mouth disc of Punctatus and its functional morphology from the earliest Cambrian of the South Shaanxi China

The Meishucun stage is the prelude in decipher-ing the Cambrian Explosion. In this prominent stage, rapid radioactive evolution and body-plan innovation have taken place and different associations of organism have been shaped. In this paper we report several 3D-preserved rare star-like fossils with finely preserved soft tissues which were recovered from the Kuanchuanpu Member of the Dengying Formation in South Shaanxi, China in 2003. By studying on functional morphology and analogy with mouthpart of Punctatus, there are evidences that this star-like organism approaches the coelenterates in systematic classification and the centre of star-like organism is its mouth. The appearance of coelenterates marks the real beginning of metazoan evolution. Therefore, it has the prominent position in the origin and evolutionary history of organisms. Perhaps the star-like organism represents the early types of coelenterate with original tentacles. These new materials provide new evidence for the origin, evolution and the functional evolution of the metazoan during the early stage of the Cambrian Explosion.     

珍稀濒危植物毛柄小勾儿茶的离体培养

以珍稀濒危植物毛柄小勾儿茶（Berchemiella wilsonii（Schneid．）Nakai var．pubipetiolata H．Qian）嫩梢为外植体进行组织培养实验,结果表明：以1／2 MS＋6-BA0．5mg／L＋NAA 0．05mg／L为芽诱导培养基、MS＋6-BA0．5mg／L＋NAA 0．05mg／L为增殖培养基,可以得到大量的毛柄小勾儿茶试管苗。     

Comparative sequencing of a microsatellite locus reveals size homoplasy within and between european oak species (<Emphasis Type="Italic">Quercus</Emphasis> spp.)

Microsatellites (simple sequence repeats [SSRs]) are highly variable molecular markers that are a rich and readily assayed source of variation for population genetic studies. Cross-amplification between closely related species is possible when there are no (or few) sequence differences in the primer binding sites. The occurrence of nonhomologous fragments of the same size (size homoplasy) is a contraint of microsatellites. Size homoplasy can be caused by insertions/deletions (indels) in SSR flanking regions. We found that size variation in locus ssrQZAG9 is due to different repeat numbers of the SSR motifs but also to indels in SSR flanking regions. Indels were found within species belonging to sectionsRobur andCerris of genusQuercus and also between species of the 2 sections. In sectionRobur (Quercis robur L.,Quercus petraea [Matt.] Liebl.,Quercus pubescens Willd.), we detected rare alleles with an indel of 57 bp or 62 bp followed by a smaller indel of 12 bp in the SSR flanking regions. These alleles show a size range overlapping with that of alleles amplified inQuercus cerris L. (sectionCerris). Multiple alignments with sequences of sectionRobur revealed the same SSR repeat motif but multiple indels in SSR flanking regions inQ. cerris. We discuss the effects of size homoplasy of SSR loci for the study of interspecific gene flow and on estimates of population differentiation.